Peatlands can export large amounts of carbon in various forms, including surface gas emissions and the discharge of dissolved carbon under aerobic/anaerobic soil degradation. Therefore, an apparent imbalance can be expected between gaseous CO2 production and O2 consumption in unsaturated peat layers. The present study monitored profiles of soil CO2 and O2 in Bibai mire, Hokkaido, Japan, with the aim of examining the apparent imbalance between the two gases. The CO2 abundance to the atmospheric level did not exceed the O2 deficit because the CO2 concentrations were 0.21, 0.75 and 2.92%, whereas the O2 concentrations were 19.71, 18.05 and 9.51% at depths of 10, 20 and 30 cm, respectively. This shortage of CO2 abundance implied that a remarkable amount of CO2 dissolved into the liquid phase. The dissolved CO2 mass on the basis of Henry's law ranged from 1.72 to 159.3 mmol m−2 (10 cm)−1, and was 1.59–5.25-fold greater than the gaseous CO2 mass. The mass balance analyses showed that the CO2 production rate in the gaseous phase at a depth of 20 cm ranged from 6.52 to 23.11 mmol m−2 (10 cm)−1 day−1, equivalent to 43% on average of the O2 consumption rate. This CO2 production rate contributed to less than 10% of the gaseous CO2 produced in the unsaturated peat layer, which had a maximum thickness of 40 cm, implying the existence of a large CO2 source in the peat layer, including in the saturated zone. The mass balance analyses also showed that the residence time of CO2 in the gaseous phase alone was 0.351 day, whereas that in the whole peat soil matrix was 0.919 day at a depth of approximately 20 cm, suggesting that high water content serves as a tentative storage for gaseous CO2 in peatlands.